Fig. 9.

Dealing with evidence from alignments. The reference genome is displayed as a thin line at the top, with an example deletion highlighted in red. Paired-end reads are displayed as two connected thick bars. Deletions within the alignment of a read are displayed as thinner region. Soft clips in the alignment are dotted. Fragment origin is encoded by color (red = variant; black = reference). a Reads coming from the variant allele can be aligned with soft-clipped ends or with the variant being encoded in the alignment itself. Due to ambiguities, the positions are not necessarily perfectly aligned with the variant (see Fig. S12 (Additional file 1) for a real example). b Depending on the size of the variant and properties of the read mapper on a specific genome, it can become less likely to obtain fragments from the variant allele. Here, the first and the second fragments are mappable, and the third is not, because the soft clip would become too large to be considered by the read mapper